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(-) Description

Title :  CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS VRSA-9 D-ALA:D-ALA LIGASE
 
Authors :  F. A. Saul, A. Haouz, D. Meziane-Cherif
Date :  28 May 10  (Deposition) - 13 Oct 10  (Release) - 13 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Vancomycin Dependence, Cell Wall Synthesis, D-Ala:D-Ala Ligase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Meziane-Cherif, F. A. Saul, C. Moubareck, P. Weber, A. Haouz, P. Courvalin, B. Perichon
Molecular Basis Of Vancomycin Dependence In Vana-Type Staphylococcus Aureus Vrsa-9.
J. Bacteriol. V. 192 5465 2010
PubMed-ID: 20729361  |  Reference-DOI: 10.1128/JB.00613-10

(-) Compounds

Molecule 1 - D-ALANINE--D-ALANINE LIGASE
    Chains: A, B
    EC Number: 6.3.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A(+)
    Expression System Strain: BL21(DE3)PLYS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DDL
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Strain: VRSA-9
    Synonym: D-ALANYLALANINE SYNTHETASE, D-ALA-D-ALA LIGASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2CL1Ligand/IonCHLORIDE ION
3SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:145 , PHE A:175 , LYS A:177 , SER A:183 , SER A:184 , ILE A:187 , GLU A:213 , GLN A:214 , GLY A:215 , VAL A:216 , GLU A:220 , PHE A:295 , ASN A:305 , GLU A:306 , HOH A:371 , SO4 A:401 , HOH A:418BINDING SITE FOR RESIDUE ANP A 400
2AC2SOFTWAREARG A:291 , ASN A:308 , PRO A:311 , GLY A:312 , HOH A:370 , ANP A:400BINDING SITE FOR RESIDUE SO4 A 401
3AC3SOFTWAREASN A:228 , ASP A:229 , TYR A:230BINDING SITE FOR RESIDUE CL A 402
4AC4SOFTWARELEU B:145 , PHE B:175 , LYS B:177 , ILE B:187 , GLU B:213 , GLN B:214 , GLY B:215 , VAL B:216 , GLU B:220 , ASN B:305 , GLU B:306 , HOH B:367BINDING SITE FOR RESIDUE ANP B 400
5AC5SOFTWAREARG B:291 , ASN B:308 , PRO B:311 , GLY B:312 , HOH B:424 , HOH B:496BINDING SITE FOR RESIDUE SO4 B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N8D)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:172 -Pro A:173
2Ile A:261 -Pro A:262
3Tyr B:172 -Pro B:173
4Ile B:261 -Pro B:262

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N8D)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DALA_DALA_LIGASE_1PS00843 D-alanine--D-alanine ligase signature 1.DDL_STAAC96-107
 		  2A:99-107
B:99-107
2DALA_DALA_LIGASE_2PS00844 D-alanine--D-alanine ligase signature 2.DDL_STAAC284-312
 		  2A:284-312
B:284-312

(-) Exons   (0, 0)

(no "Exon" information available for 3N8D)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:329
 aligned with DDL_STAAC | Q5HEB7 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:352
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351  
            DDL_STAAC     2 TKENICIVFGGKSAEHEVSILTAQNVLNAIDKDKYHVDIIYITNDGDWRKQNNITAEIKSTDELHLENGEALEISQLLKESSSGQPYDAVFPLLHGPNGEDGTIQGLFEVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKYEHNILKLVNDKLNYPVFVKPANLGSSVGISKCNNEAELKEGIKEAFQFDRKLVIEQGVNAREIEVAVLGNDYPEATWPGEVVKDVAFYDYKSKYKDGKVQLQIPADLDEDVQLTLRNMALEAFKATDCSGLVRADFFVTEDNQIYINETNAMPGFTAFSMYPKLWENMGLSYPELITKLIELAKERHQDKQKNKY 353
               SCOP domains d3n8da1 A:2-128 automated matches                                                                                              d3n8da2 A:129-353 automated matches                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhhhhhh....eeeeeeee.....eeee........hhhhhh..----.hhhhhhhh........eeee..---....hhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhh...eeeee.........eee.hhhhhhhhhhhhh....eeeeee....eeeeeeeee....ee...eee.----------------..ee.....hhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeee........hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------DALA_DALA_LI--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2           ----------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n8d A   2 TKENICIVFGGKSAEHEVSILTAQNVLNAIDKDKYHVDIIYITNDGDWRKQNNITAEIKSTDELHLE----LEISQLLKESSSGQPYDAVFPLL---NGEDGTIQGLFEVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKYEHNILKLVNDKLNYPVFVKPANLGSSVGISKCNNEAELKEGIKEAFQFDRKLVIEQGVNAREIEVAVLGNDYPEATWPGEVV----------------VQLKIPADLDEDVQLTLRNMALEAFKETDCSGLVRADFFVTEDNQIYINETNAMPGFTAFSMYPKLWENMGLSYPELITKLIELAKERHQDKQKNKY 353
                                    11        21        31        41        51        61      |  - |      81        91   |   101       111       121       131       141       151       161       171       181       191       201       211       221       231        |-         -     | 261       271       281       291       301       311       321       331       341       351  
                                                                                             68   73                    95  99                                                                                                                                          240              257                                                                                                


Chain B from PDB  Type:PROTEIN  Length:334
 aligned with DDL_STAAC | Q5HEB7 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:357
                                                                                                                                                                                                                                                                                                                                                                                            356  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351    |  
            DDL_STAAC     2 TKENICIVFGGKSAEHEVSILTAQNVLNAIDKDKYHVDIIYITNDGDWRKQNNITAEIKSTDELHLENGEALEISQLLKESSSGQPYDAVFPLLHGPNGEDGTIQGLFEVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKYEHNILKLVNDKLNYPVFVKPANLGSSVGISKCNNEAELKEGIKEAFQFDRKLVIEQGVNAREIEVAVLGNDYPEATWPGEVVKDVAFYDYKSKYKDGKVQLQIPADLDEDVQLTLRNMALEAFKATDCSGLVRADFFVTEDNQIYINETNAMPGFTAFSMYPKLWENMGLSYPELITKLIELAKERHQDKQKNKYKID--   -
               SCOP domains d3n8db1 B:2-128 automated matches                                                                                              d3n8db2 B:129-358 automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Dala_Dala_lig_N-3n8dB03 B:4-119                                                                                     ----------------Dala_Dala_lig_C-3n8dB01 B:136-339                                                                                                                                                                           ------------------- Pfam domains (1)
           Pfam domains (2) --Dala_Dala_lig_N-3n8dB04 B:4-119                                                                                     ----------------Dala_Dala_lig_C-3n8dB02 B:136-339                                                                                                                                                                           ------------------- Pfam domains (2)
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhhhh......eeeeeeee.....eeee........hhhhhh..-----hhhhhhh.........eeee..---....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhh...eeeee...---...eee.hhhhhhhhhhhhhhhh.eeeeee....eeeeeeeee....ee...eee......------------.ee.....hhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeee........hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------DALA_DALA_LI--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2           ---------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n8d B   2 TKENICIVFGGKSAEHEVSILTAQNVLNAIDKDKYHVDIIYITNDGDWRKQNNITAEIKSTDELHLE-----EISQLLKESSSGQPYDAVFPLL---NGEDGTIQGLFEVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKYEHNILKLVNDKLNYPVFVKPANL---VGISKCNNEAELKEGIKEAFQFDRKLVIEQGVNAREIEVAVLGNDYPEATWPGEVVKDVAF------------QLKIPADLDEDVQLTLRNMALEAFKETDCSGLVRADFFVTEDNQIYINETNAMPGFTAFSMYPKLWENMGLSYPELITKLIELAKERHQDKQKNKYKIDLE 358
                                    11        21        31        41        51        61      |  -  |     81        91   |   101       111       121       131       141       151       161       171       181   |   191       201       211       221       231       241   |     -      |261       271       281       291       301       311       321       331       341       351       
                                                                                             68    74                   95  99                                                                               181 185                                                         245          258
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N8D)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: ATP-grasp (83)
(-)
Clan: no clan defined [family: Dala_Dala_lig_N] (12)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DDL_STAAC | Q5HEB7)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008716    D-alanine-D-alanine ligase activity    Catalysis of the reaction: 2 D-alanine + ATP = D-alanyl-D-alanine + ADP + 2 H(+) + phosphate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DDL_STAAC | Q5HEB7: 2i80 2i87 2i8c

(-) Related Entries Specified in the PDB File

2i80 2i87 2i8c